RT Journal Article
SR Electronic
T1 Succinct Colored de Bruijn Graphs
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 040071
DO 10.1101/040071
A1 Keith Belk
A1 Christina Boucher
A1 Alexander Bowe
A1 Travis Gagie
A1 Paul Morley
A1 Martin D. Muggli
A1 Noelle R. Noyes
A1 Simon J. Puglisi
A1 Rober Raymond
YR 2016
UL http://biorxiv.org/content/early/2016/02/18/040071.abstract
AB Iqbal et al. (Nature Genetics, 2012) introduced the colored de Bruijn graph, a variant of the classic de Bruijn graph, which is aimed at “detecting and genotyping simple and complex genetic variants in an individual or population”. Because they are intended to be applied to massive population level data, it is essential that the graphs be represented efficiently. Unfortunately, current succinct de Bruijn graph representations are not directly applicable to the colored de Bruijn graph, which require additional information to be succinctly encoded as well as support for non-standard traversal operations. Our data structure dramatically reduces the amount of memory required to store and use the colored de Bruijn graph, with some penalty to runtime, allowing it to be applied in much larger and more ambitious sequence projects than was previously possible.